Search results for: SPIKE PROTEIN, SARS-COV-2, T-SNE ALGORITHM, CLASSIFICATION
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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The use of fast molecular descriptors and artificial neural networks approach in organochlorine compounds electron ionization mass spectra classification
PublicationDeveloping of theoretical tools can be very helpful for supporting new pollutant detection. Nowadays, a combination of mass spectrometry and chromatographic techniques are the most basic environmental monitoring methods. In this paper, two organochlorine compound mass spectra classification systems were proposed. The classification models were developed within the framework of artificial neural networks (ANNs) and fast 1D and...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Better polynomial algorithms for scheduling unit-length jobs with bipartite incompatibility graphs on uniform machines
PublicationThe goal of this paper is to explore and to provide tools for the investigation of the problems of unit-length scheduling of incompatible jobs on uniform machines. We present two new algorithms that are a significant improvement over the known algorithms. The first one is Algorithm 2 which is 2-approximate for the problem Qm|p j = 1, G = bisubquartic|Cmax . The second one is Algorithm 3 which is 4-approximate for the problem Qm|p...
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Application of Intuitionistic Fuzzy Sets to the assessment of technical university students
PublicationThe article proposes application of artificial intelligence methods to assess students of technical universities. The level of achieved educational goals can be assessed using measurements based on the idea of Fuzzy Intuitionistic Sets (IFS). A classification algorithm was developed and an exemplary distribution of the criteria values using IFS was presented. The application of the proposed approach in online education can enrich...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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0-step K-means for clustering Wikipedia search results
PublicationThis article describes an improvement for K-means algorithm and its application in the form of a system that clusters search results retrieved from Wikipedia. The proposed algorithm eliminates K-means isadvantages and allows one to create a cluster hierarchy. The main contributions of this paper include the ollowing: (1) The concept of an improved K-means algorithm and its application for hierarchical clustering....
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Music genre classification applied to bass enhancement for mobile technology
PublicationThe aim of this paper is to present a novel approach to the Virtual Bass Synthesis (VBS) algorithms applied to portable computers. The proposed algorithm is related to intelligent, rule-based setting of synthesis parameters according to music genre of an audio excerpt. The classification of music genres is automatically executed employing MPEG 7 parameters and the Principal Component Analysis method applied to reduce information...
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Speech Analytics Based on Machine Learning
PublicationIn this chapter, the process of speech data preparation for machine learning is discussed in detail. Examples of speech analytics methods applied to phonemes and allophones are shown. Further, an approach to automatic phoneme recognition involving optimized parametrization and a classifier belonging to machine learning algorithms is discussed. Feature vectors are built on the basis of descriptors coming from the music information...
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System for characterisation and multidimensional imaging of seafloor using multibeam sonar data
PublicationMultibeam sonars are widely used in applications like high resolution bathymetry measurements, underwater object detection and imaging, etc. Also, they are the promising tool in seafloor characterisation and classification, having several advantages over conventional single beam echosounders. The proposed approach to seafloor classification relies on the combined use of three different techniques. In each of them, a set of descriptors...
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Trees having many minimal dominating sets
PublicationWe provide an algorithm for listing all minimal dominating sets of a tree of order n in time O(1.4656^n). This leads to that every tree has at most 1.4656^n minimal dominating sets. We also give an infinite family of trees of odd and even order for which the number of minimal dominating sets exceeds 1.4167^n, thus exceeding 2^{n/2}. This establishes a lower bound on the running time of an algorithm for listing all minimal dominating...
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Wild oscillations in a nonlinear neuron model with resets: (II) Mixed-mode oscillations
PublicationThis work continues the analysis of complex dynamics in a class of bidimensional nonlinear hybrid dynamical systems with resets modeling neuronal voltage dynamics with adaptation and spike emission. We show that these models can generically display a form of mixed-mode oscillations (MMOs), which are trajectories featuring an alternation of small oscillations with spikes or bursts (multiple consecutive spikes). The mechanism by...
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Determining the optimal filling of the surface with a linker with Universal Force Field and Reax Force Field
Open Research DataThe DataSet contains the atomic slabs of diamond surfaces with ATP molecules in water. The calculated data includes different sized surfaces from 90 Angstrom^2 to 691 Angstrom^2. Structures were relaxed using the Reax Force Field method with the Limited Memory Broyden–Fletcher–Goldfarb–Shanno algorithm. Structures were calculated with a convergence...
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Minimal 2-dominating sets in Trees
PublicationWe provide an algorithm for listing all minimal 2-dominating sets of a tree of order n in time O(1.3247^n). This leads to that every tree has at most 1.3247^n minimal 2-dominating sets. We also show that thisbound is tight.
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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An Approach to Bass Enhancement in Portable Computers Employing Smart Virtual Bass Synthesis Algorithms
PublicationThe aim of this paper is to present a novel approach to the Virtual Bass Synthesis (VBS) algorithms applied to portable computers. The developed algorithms are related to intelligent, rule-based setting of synthesis parameters according to music genre of an audio excerpt and to the type of a portable device in use. To find optimum synthesis parameters of the VBS algorithms, subjective listening tests based on a parametric procedure...
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Segmentation-Based BI-RADS ensemble classification of breast tumours in ultrasound images
PublicationBackground: The development of computer-aided diagnosis systems in breast cancer imaging is exponential. Since 2016, 81 papers have described the automated segmentation of breast lesions in ultrasound images using arti- ficial intelligence. However, only two papers have dealt with complex BI-RADS classifications. Purpose: This study addresses the automatic classification of breast lesions into binary classes (benign vs. ma- lignant)...
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Marta Kuc-Czarnecka dr
PeopleMarta Kuc-Czarnecka is the deputy head of the Department of Statistics and Economics at the Faculty of Management and Economics of the Gdańsk University of Technology. She also serves as the Dean's proxy for AMBA accreditation. She is a co-founder of Rethinking Economics Gdańsk and a member of the Foundation Edward Lipiński for the promotion of pluralism in economic sciences. In 2018-2022, she was Eurofound’s quality of life and...
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Further developments of parameterization methods of audio stream analysis for secuirty purposes
PublicationThe paper presents an automatic sound recognition algorithm intended for application in an audiovisual security monitoring system. A distributed character of security systems does not allow for simultaneous observation of multiple multimedia streams, thus an automatic recognition algorithm must be introduced. In the paper, a module for the parameterization and automatic detection of audio events is described. The spectral analyses...
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Multimodal Particle Swarm Optimization with Phase Analysis to Solve Complex Equations of Electromagnetic Analysis
PublicationIn this paper, a new meta-heuristic method of finding roots and poles of a complex function of a complex variable is presented. The algorithm combines an efficient space exploration provided by the particle swarm optimization (PSO) and the classification of root and pole occurrences based on the phase analysis of the complex function. The method initially generates two uniformly distributed populations of particles on the complex...
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Categorization of Cloud Workload Types with Clustering
PublicationThe paper presents a new classification schema of IaaS cloud workloads types, based on the functional characteristics. We show the results of an experiment of automatic categorization performed with different benchmarks that represent particular workload types. Monitoring of resource utilization allowed us to construct workload models that can be processed with machine learning algorithms. The direct connection between the functional...
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Harmony Search for Data Mining with Big Data
PublicationIn this paper, some harmony search algorithms have been proposed for data mining with big data. Three areas of big data processing have been studied to apply new metaheuristics. The first problem is related to MapReduce architecture that can be supported by a team of harmony search agents in grid infrastructure. The second dilemma involves development of harmony search in preprocessing of data series before data mining. Moreover,...
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On-line ranking of split graphs
PublicationA vertex ranking of a graph G is an assignment of positive integers (colors) to the vertices of G such that each path connecting two vertices of the same color contains a vertex of a higher color. Our main goal is to find a vertex ranking using as few colors as possible. Considering on-line algorithms for vertex ranking of split graphs, we prove that the worst case ratio of the number of colors used by any on-line ranking algorithm...
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Pilicides effectively hinder chaperone-usher interactions in all Gram-negative bacteria
PublicationThe chaperone-usher pathway of adhesive structures biogenesis is highly conserved in all Gram-negative bacteria. Pili are polymers of thousands protein subunits that possess conserved immunoglobuline-like structure denoted by lack of the seventh G strand. The effect of this structural defect is a hydrophobic acceptor cleft. The folding of protein subunits is strictly dependent on the action of specific periplasmic chaperone protein...
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Enzymatic activities behind degradation of glucosinolates
PublicationMyrosinase (thioglucosidase, EC 3.2.1.147) is the enzyme responsible for the hydrolysis of glucosinolates (GLs). In plant tissue, myrosinase and GLs are sequestered in separate cellular compartments. As a result of cell disruption, e.g., after pathogen attack or on chopping or grinding during food preparation, the myrosinase comes into contact with GLs and catalyzes the hydrolysis of thioglucosidic bond in GL structure. Consequently,...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublicationApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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Inhibition of amyloid fibril formation of hen egg white lysozyme by trimethylamine N-oxide at low pH
PublicationIn vitro inhibition of the formation of fibrous aggregates of proteins (amyloids) has gained increasing attention due to the number of diseases associated with protein misfolding and fibrillation. An interesting group of compounds for which pronounced activity against this phenomenon can be expected consists of low molecular weight substances (osmolytes) which have the ability to change protein stability. Here we investigate the...
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Ranking Speech Features for Their Usage in Singing Emotion Classification
PublicationThis paper aims to retrieve speech descriptors that may be useful for the classification of emotions in singing. For this purpose, Mel Frequency Cepstral Coefficients (MFCC) and selected Low-Level MPEG 7 descriptors were calculated based on the RAVDESS dataset. The database contains recordings of emotional speech and singing of professional actors presenting six different emotions. Employing the algorithm of Feature Selection based...
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Monitoring of odour nuisance in the Tricity Agglomeration
PublicationThe paper describes a principle of operation of odour nuisance monitoring network, which is being designed in the Tricity Agglomeration. Moreover, it presents the preliminary results of an investigation on ambient air quality with respect to odour nuisance in a vicinity of the municipal landfill. The investigation was performed during spring-winter season using a prototype of electronic nose and the Nasal Ranger field olfactometers. The...
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Comparison of the measurement techniques employed for evaluation of ambient air odour quality
PublicationThe paper presents the results of investigation on ambient air odour quality in a vicinity of the industrial sewage treatment plant being a part of the crude oil processing plant. The investigation was performed during spring-winter season using a prototype of electronic nose and the Nasal Ranger field olfactometers. The prototype was equipped with a set of six semiconductor sensors by FIGARO Co. and one PID-type sensor. The field...
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Rapid Evaluation of Poultry Meat Shelf Life Using PTR-MS
PublicationThe use of proton transfer reaction mass spectrometry (PTR-MS) for freshness classification of chicken and turkey meat samples was investigated. A number of volatile organic compounds (VOCs) were selected based on the correlation (> 95%) of their concentration during storage at 4 °C over a period of 5 days with the results of the microbial analysis. In order to verify if the selected compounds are not sample-specific, a number...
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A review on computer‐aided chemogenomics and drug repositioning for rational COVID ‐19 drug discovery
PublicationApplication of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development...
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Classification of Polish wines by application of ultra-fast gas chromatography
PublicationThe potential of ultra-fast gas chromatography (GC) combined with chemometric analysis for classification of wine originating from Poland according to the variety of grape used for production was investigated. A total of 44 Polish wine samples differing in the type of grape (and grape growth region) used for the production as well as parameters of the fermentation process, alcohol content, sweetness, and others which characterize...
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Weekend Muzeów online na Politechnice Gdańskiej
EventsZapraszamy do udziału w Weekendzie Muzeów – wykładach online, podejmujących aktualne zagadnienia zdrowotne. Transmisja na żywo na kanale YouTube Politechnika Otwarta, z możliwością zadawania pytań prelegentom w komentarz
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Malignant lymphoma, large B-cell, diffuse, centroblastic, NOS - Female, 72 - Tissue image [9300729527457751]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Malignant lymphoma, large B-cell, diffuse, centroblastic, NOS - Female, 72 - Tissue image [9300729527452191]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Malignant lymphoma, large B-cell, diffuse, centroblastic, NOS - Female, 72 - Tissue image [9300729527453631]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Shared processor scheduling
PublicationWe study the shared processor scheduling problem with a single shared processor to maximize total weighted overlap, where an overlap for a job is the amount of time it is processed on its private and shared processor in parallel. A polynomial-time optimization algorithm has been given for the problem with equal weights in the literature. This paper extends that result by showing an (log)-time optimization algorithm for a class...
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B-GALACTOSIDASE ARTHROBACTER SP. 32cB - OBTAINING THE GENE SEQUENCE, CONSTRUCTION OF THE EXPRESSION SYSTEM, BIOSYNTHESIS AND BIOCHEMICAL CHARACTERIZATION OF THE ENZYME
PublicationINTRODUCTION: β-Galactosidase is an enzyme which catalyzes the hydrolysis of O glycosidic bond in β-galactosides. Another activity of β galactosidase is a transglycosylation activity. The main industrial use of this protein is the hydrolysis of lactose in milk in a cooling conditions. Synthesis of galactooligosaccharides, which are mostly used as a prebiotics added to some foods or available as dietary supplements, is only one...
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A space-efficient algorithm for computing the minimum cycle mean in a directed graph
PublicationAn algorithm is introduced for computing the minimum cycle mean in a strongly connected directed graph with n vertices and m arcs that requires O(n) working space. This is a considerable improvement for sparse graphs in comparison to the classical algorithms that require O(n^2) working space. The time complexity of the algorithm is still O(nm). An implementation in C++ is made publicly available at http://www.pawelpilarczyk.com/cymealg/.
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Evaluation of a Novel Approach to Virtual Bass Synthesis Strategy
PublicationThe aim of this paper is to present a novel approach to the Virtual Bass Synthesis (VBS) strategy applied to portable computers. The developed algorithms involve intelligent, rule-based settings of bass synthesis parameters with regard to music genre of an audio excerpt and the type of a portable device in use. The Smart VBS algorithm performs the synthesis based on a nonlinear device (NLD) with artificial controlling synthesis...
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Improving the Accuracy in Sentiment Classification in the Light of Modelling the Latent Semantic Relations
PublicationThe research presents the methodology of improving the accuracy in sentiment classification in the light of modelling the latent semantic relations (LSR). The objective of this methodology is to find ways of eliminating the limitations of the discriminant and probabilistic methods for LSR revealing and customizing the sentiment classification process (SCP) to the more accurate recognition of text tonality. This objective was achieved...
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Open-Set Speaker Identification Using Closed-Set Pretrained Embeddings
PublicationThe paper proposes an approach for extending deep neural networks-based solutions to closed-set speaker identification toward the open-set problem. The idea is built on the characteristics of deep neural networks trained for the classification tasks, where there is a layer consisting of a set of deep features extracted from the analyzed inputs. By extracting this vector and performing anomaly detection against the set of known...
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External Validation Measures for Nested Clustering of Text Documents
PublicationAbstract. This article handles the problem of validating the results of nested (as opposed to "flat") clusterings. It shows that standard external validation indices used for partitioning clustering validation, like Rand statistics, Hubert Γ statistic or F-measure are not applicable in nested clustering cases. Additionally to the work, where F-measure was adopted to hierarchical classification as hF-measure, here some methods to...
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Predicting emotion from color present in images and video excerpts by machine learning
PublicationThis work aims at predicting emotion based on the colors present in images and video excerpts using a machine-learning approach. The purpose of this paper is threefold: (a) to develop a machine-learning algorithm that classifies emotions based on the color present in an image, (b) to select the best-performing algorithm from the first phase and apply it to film excerpt emotion analysis based on colors, (c) to design an online survey...
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Wireless Body Area Network for Preventing Self-Inoculation Transmission of Respiratory Viral Diseases
PublicationThis paper proposes an idea of Wireless Body Area Networks (WBANs) based on Bluetooth Low-Energy (BLE) standards to recognize and alarm a gesture of touching the face, and in effect, to prevent self-inoculation of respiratory viral diseases, such as COVID-19 or influenza A, B, or C. The proposed network comprises wireless modules placed in bracelets and a necklace. It relies on the received signal strength indicator (RSSI) measurements...
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Improving css-KNN Classification Performance by Shifts in Training Data
PublicationThis paper presents a new approach to improve the performance of a css-k-NN classifier for categorization of text documents. The css-k-NN classifier (i.e., a threshold-based variation of a standard k-NN classifier we proposed in [1]) is a lazy-learning instance-based classifier. It does not have parameters associated with features and/or classes of objects, that would be optimized during off-line learning. In this paper we propose...
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Comparison of the effectiveness of automatic EEG signal class separation algorithms
PublicationIn this paper, an algorithm for automatic brain activity class identification of EEG (electroencephalographic) signals is presented. EEG signals are gathered from seventeen subjects performing one of the three tasks: resting, watching a music video and playing a simple logic game. The methodology applied consists of several steps, namely: signal acquisition, signal processing utilizing z-score normalization, parametrization and...
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Vehicle classification based on soft computing algorithms
PublicationExperiments and results regarding vehicle type classification are presented. Three classes of vehicles are recognized: sedans, vans and trucks. The system uses a non-calibrated traffic camera, therefore no direct vehicle dimensions are used. Various vehicle descriptors are tested, including those based on vehicle mask only and those based on vehicle images. The latter ones employ Speeded Up Robust Features (SURF) and gradient images...
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LSTM-based method for LOS/NLOS identification in an indoor environment
PublicationDue to the multipath propagation, harsh indoor environment significantly impacts transmitted signals which may adversely affect the quality of the radiocommunication services, with focus on the real-time ones. This negative effect may be significantly reduced (e.g. resources management and allocation) or compensated (e.g. correction of position estimation in radiolocalisation) by the LOS/NLOS identification algorithm. This paper...